[English] 日本語
Yorodumi
- PDB-1ep3: CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGEN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ep3
TitleCRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS.
Components(DIHYDROOROTATE DEHYDROGENASE B ...) x 2
KeywordsOXIDOREDUCTASE / Heterotetramer / ALPHA-BETA barrel / BETA sandwich / FAD domain / ALPHA/BETA NADP domain / FeS cluster binding domain
Function / homology
Function and homology information


dihydroorotate dehydrogenase (NAD+) / dihydroorotate dehydrogenase (NAD+) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / oxidoreductase activity / electron transfer activity / metal ion binding / cytoplasm
Similarity search - Function
: / : / Dihydroorotate dehydrogenase B (pyrk subunit); domain 3 / Dihydroorotate dehydrogenase, electron transfer subunit / Dihydroorotate dehydrogenase electron transfer subunit / Dihydroorotate dehydrogenase, class 1B / Dihydroorotate dehydrogenase, electron transfer subunit, Fe-S binding domain superfamily / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B ...: / : / Dihydroorotate dehydrogenase B (pyrk subunit); domain 3 / Dihydroorotate dehydrogenase, electron transfer subunit / Dihydroorotate dehydrogenase electron transfer subunit / Dihydroorotate dehydrogenase, class 1B / Dihydroorotate dehydrogenase, electron transfer subunit, Fe-S binding domain superfamily / Cytochrome-c3 hydrogenase, gamma subunit / Dihydroorotate dehydrogenase, electron transfer subunit, iron-sulphur cluster binding domain / Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B / Dihydroorotate dehydrogenase, class 1 / Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Ribbon / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit / Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRowland, P. / Norager, S. / Jensen, K.F. / Larsen, S.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster.
Authors: Rowland, P. / Norager, S. / Jensen, K.F. / Larsen, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminary X-ray Diffraction Analysis of the Heterotetrameric Dihydroorotate Dehydrogenase B of Lactococcus lactis, a Flavoprotein Enzyme System Consisting of two PyrDB ...Title: Crystallization and Preliminary X-ray Diffraction Analysis of the Heterotetrameric Dihydroorotate Dehydrogenase B of Lactococcus lactis, a Flavoprotein Enzyme System Consisting of two PyrDB Subunits and Two Iron-Sulfur Cluster Containing PyrK Subunits
Authors: Rowland, P. / Nielsen, F.S. / Jensen, K.F. / Larsen, S.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: The B Form of Dihydroorotate Dehydrogenase from Lactococcus lactis Consists of two Different Subunits, Encoded by the pyrDb and PyrK Genes, and Contains FMN, FAD and [FeS] Redox Centers
Authors: Nielsen, F.S. / Andersen, P.S. / Jensen, K.F.
#3: Journal: Flavins and Flavoproteins / Year: 1999
Title: Roles of three prosthetic groups in tetrameric Dihydroorotate dehydrogenase B from Lactococcus lactis
Authors: Jensen, K.F. / Bjornberg, O. / Nielsen, F.S. / Ottosen, M. / Sorensen, P.G. / Rowland, P. / Norager, S. / Larsen, S.
History
DepositionMar 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
B: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0855
Polymers61,6682
Non-polymers1,4183
Water8,395466
1
A: DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
B: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
hetero molecules

A: DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
B: DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,17110
Polymers123,3354
Non-polymers2,8356
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+11
Buried area13990 Å2
ΔGint-110 kcal/mol
Surface area41350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)199.89, 199.89, 80.27
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-578-

HOH

-
Components

-
DIHYDROOROTATE DEHYDROGENASE B ... , 2 types, 2 molecules AB

#1: Protein DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)


Mass: 32977.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P54322, EC: 1.3.3.1
#2: Protein DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)


Mass: 28690.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P56968, EC: 1.3.3.1

-
Non-polymers , 4 types, 469 molecules

#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2.1 - 2.4 M Ammonium sulfate, 0.1 M Na-acetate pH 4 to 5, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6
Details: Rowland, P., (1997) Acta Crystallogr., Sect.D, 53, 802.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
250 mMsodium phosphate1drop
310 %glycerol1drop
42.4 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8469
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8469 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 270295 / Num. obs: 35821 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16.62
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.327 / Num. unique all: 1554 / % possible all: 87.5
Reflection
*PLUS
Num. measured all: 270295

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1EP1

1ep1


Resolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3509 10 %RANDOM
Rwork0.195 ---
all-35305 --
obs-35305 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.1266 Å2 / ksol: 0.374949 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 88 466 4854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009084
X-RAY DIFFRACTIONc_angle_deg1.42637
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.13892
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 584 10.3 %
Rwork0.251 5106 -
obs--96 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13892
LS refinement shell
*PLUS
Rfactor Rfree: 0.295 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.251

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more